Update snakemake to 8.25.3

[BiocondaBot]

Update snakemake: 8.25.2 → 8.25.3

Info	Link or Description
Recipe	recipes/snakemake (click to view/edit other files)
Summary	A popular workflow management system aiming at full in-silico reproducibility.
Home	https://snakemake.github.io
Releases	https://pypi.org/pypi/snakemake/json
Recipe Maintainer(s)	@johanneskoester, @corneliusroemer

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This pull request was automatically generated (see docs).

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request involves an update to the meta.yaml file for the Snakemake package. The version number has been changed from 8.25.2 to 8.25.3, and the source URL has been updated to point to the new version's tarball. Additionally, the SHA256 checksum has been modified to ensure the integrity of the new package version. The requirements section shows that the run dependencies remain mostly unchanged, still referencing the updated version of snakemake-minimal. The test commands have been preserved, ensuring that the version check for Snakemake is consistent with the new version. Overall, the changes focus on versioning and maintaining package integrity through the updated checksum.

Possibly related PRs

• Update snakemake to 8.25.0 #51767: This PR updates the version of Snakemake from 8.24.1 to 8.25.0, which is directly related to the main PR that updates the version from 8.25.2 to 8.25.3.
• Update snakemake to 8.25.1 #51871: This PR updates the version of Snakemake from 8.25.0 to 8.25.1, which is also directly related to the main PR that updates the version from 8.25.2 to 8.25.3.

Suggested reviewers

• johanneskoester

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 3d83203 and 152b3b8.

📒 Files selected for processing (1)

• recipes/snakemake/meta.yaml (1 hunks)

🔇 Additional comments (4)

recipes/snakemake/meta.yaml (4)

Line range hint 20-33: Dependencies are well-structured and properly constrained

The dependencies are well-organized with:

• Clear version constraints
• Documented Python version requirements
• Properly pinned interface plugin versions

Also applies to: 91-124

🧰 Tools

🪛 yamllint

[error] 3-3: syntax error: found character '%' that cannot start any token

(syntax)

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Line range hint 35-41: Test commands are comprehensive and well-structured

The test suite includes:

• Version verification
• Report generation to validate dependencies
• Proper cleanup of test artifacts

Also applies to: 126-131

🧰 Tools

🪛 yamllint

[error] 3-3: syntax error: found character '%' that cannot start any token

(syntax)

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4-4: Verify dependencies against upstream setup.cfg

As per the comment at the top of the file, we should verify that the dependencies match the upstream setup.cfg for version 8.25.3.

✅ Verification successful

Dependencies are correctly synchronized with upstream

After comparing the dependencies in meta.yaml with upstream setup.cfg for version 8.25.3:

• All core dependencies from setup.cfg's install_requires are present in meta.yaml with matching version constraints
• Optional dependencies (messaging, pep, reports) are also correctly included
• Python version requirement (>=3.11,<3.13) is properly specified

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify dependencies match upstream setup.cfg
# Fetch setup.cfg from snakemake repo for version 8.25.3
curl -sL "https://raw.githubusercontent.com/snakemake/snakemake/v8.25.3/setup.cfg" | grep -A 50 "install_requires ="

Length of output: 1176

---

Script:

#!/bin/bash
# Get dependencies from meta.yaml for comparison
cat recipes/snakemake/meta.yaml | grep -A 50 "requirements:"

Length of output: 3231

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12-12: Verify SHA256 checksum against PyPI package

Let's ensure the SHA256 checksum matches the package from PyPI.

---

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